ArticleNature methods2017
Reversed graph embedding resolves complex single-cell trajectories.
Article in Nature methods, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3,101 papers.
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Who cites it
3,101 citing papers in PubMed.
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- scCADI: Cell-Aware Diffusion Model for Single-Cell RNA-seq Imputation.Interdisciplinary sciences, computational life sciences · 2026Article
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- Decoding epithelial-mesenchymal transitions with multi-omics.Nature reviews. Genetics · 2026Review
- ZBP1-driven PANoptosis in granulosa cells mediates follicular arrest in PCOS: integrated transcriptomic evidence and baicalin's therapeutic potential.Naunyn-Schmiedeberg's archives of pharmacology · 2026Article
- Integrative Single-Cell Transcriptomics, Multi-Omics Analyses, and Computational Pharmacology Reveal Macrophage Heterogeneity and the Putative THBS1-CD36 Axis in Coronary Atherosclerosis.Chemical biology & drug design · 2026Article
- Intrathecal Allogeneic B7-H3-Targeted CAR γδ T Cells for Leptomeningeal Metastasis from Solid Tumors: Safety, Efficacy, and Immunologic Dynamics in a Phase I Trial.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026Article
- MSC C1: A Potential Hub Linking Stromal Plasticity, Immune Regulation, and Patient Survival in Lung Adenocarcinoma.Chemical biology & drug design · 2026Article
- Inhibition of Hexokinase 2 Undermines Cartilage Health and Accelerates Osteoarthritis.Cartilage · 2026Article
3,041 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
Abstract
Single-cell trajectories can unveil how gene regulation governs cell fate decisions. However, learning the structure of complex trajectories with multiple branches remains a challenging computational problem. We present Monocle 2, an algorithm that uses reversed graph embedding to describe multiple fate decisions in a fully unsupervised manner. We applied Monocle 2 to two studies of blood development and found that mutations in the genes encoding key lineage transcription factors divert cells to alternative fates.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.